title: Energy evaluation of β-strand packing in a fibril-forming SH3 domain.
abstract: We examine the energetics of β-strand packing in a fibril-forming SH3 domain using a simple sequence-based energy model. First, we describe this packing energy function and then apply it to three model systems: Aβ, HET-s prion, and SH3 domain. The packing results of Aβ and HET-s are compared to and are consistent with available experimental and computational results. Moreover, our results show that a native β-strand in SH3 is strongly disfavored to pack with any other strand, in accord with recent NMR data. Finally, based on packing energy calculations, several SH3 models of β-strand packing are proposed that fit well with known electron microscopy maps.
authors.affiliation: Center for Proteomics and Department of Pharmacology, Case Western Reserve University , Cleveland, Ohio, United States.
authors.forename: Sichun
authors.initials: S
authors.lastname: Yang
authors.forename: Krishnakumar M
authors.initials: KM
authors.lastname: Ravikumar
authors.forename: Herbert
authors.initials: H
authors.lastname: Levine
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry / Q000378:metabolism; D011328:Prions / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D018909:src Homology Domains
chemical_list: D016229:Amyloid beta-Peptides; D011328:Prions; D019869:Phosphatidylinositol 3-Kinases